The goal of our laboratory is to understand how genes are controlled during development. We are studying the Drosophila engrailed (en) gene. en is important for proper segmentation of the embryo and also for proper formation of the adult. en expression patterns reflect the multiple roles it plays during development. en is expressed in stripes throughout embryonic development, as well as in specific cells in the developing nervous system, head and tail, and the progenitors of the adult tissue (in the imaginal discs). We are interested in how this complex expression pattern is regulated. Spatially and temporally regulated transcription relies on positive and negative cis-acting sequences called enhancers and silencers. At least for transcriptional enhancers, these sequences can be located many tens of kilobases away on the DNA. For the engrailed (en) locus of Drosophila melanogaster, sequences located up to 40 kb upstream and 20 kb downstream of the promoter are thought to regulate transcription. The problem of how such distantly located regulatory elements influence transcription is largely unsolved. One model is that proteins bound near the promoter interact with proteins bound to the enhancer and cause a looping of intervening DNA. At en, this model requires the interaction of proteins bound to sites separated by large distances on a linear scale. One might imagine that the same proteins could mediate an interaction between noncontiguous pieces of DNA. We have identified en regulatory DNA which we postulate has the ability to do just that: first, it promotes interactions between transposons located on homologous chromosomes and second, it directs P elements to particular regions of the Drosophila genome. During the past year we have identified three sites in en DNA (called pairing-sensitive sites, PSS) which mediate interactions between transposons present on homologous chromosomes. We have also identified PSS sites within other genomic DNA. In transgenic flies, an interaction between transposon- encoded and genomic-encoded PSS sites is important for the pattern of expression of the transposon-encoded gene. These studies provide insight into mechanisms which govern expression of exogenously-added genes in transgenic organisms. The study of gene expression in transgenic animals provides insight into expression of foreign genes in human gene therapy.